Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • How to align contigs without reference genome?

    I have 53 samples which belongs to two treatments. In each sample, I started with 2X100 Illumina metagenomic data and have used SOAPdenovo2 to generated contigs. I want to combine all contigs (>10000bp) from all samples and align all contigs. I want to have alignment map or contigs map. Final goal is to find contigs which are unique to each treatment. I have no idea how to do it? Could anybody help me?

  • #2
    One of my programs, Dedupe (packaged together with BBMap), is designed to find duplicate and unique contigs. You can run it like this:

    dedupe.sh in=assembly1.fa,assembly2.fa,assembly3.fa out=unique.fa uniqueonly=t

    Optionally, you can allow some mismatches, edits, or set various other constraints.

    That will output all of the unique stuff and throw away anything with any duplicates. You should first rename the contigs so you know which assembly they came from. If you only have 2 treatments, I would suggest first merging all of the reads from a treatment and assembling them together so you only have 2 assemblies (if I correctly understand your problem).

    Comment


    • #3
      You could also try a 'superassembly' using cortex: http://cortexassembler.sourceforge.net/

      Comment


      • #4
        Thanks. Cortex assembles multiple eukaryotic genomes. But I work on microbiome.

        Comment


        • #5
          Thanks, Brian.
          I'm trying to align contains from different metagenomes to define a “Core” and looking to do at the contig level for richer genome organization and origin context.
          Do you know how to do it?

          Comment


          • #6
            Hmmm... other than dedupe, I don't really have any relevant tools. I'm not sure how to best go about that; you might need to write something yourself.

            As for dedupe, you could process all the assemblies together, allow some edit distance, set "uniqueonly=t", and set the "outd" flag to save all of the duplicate contigs. For example:

            dedupe.sh in=assembly1.fa,assembly2.fa,assembly3.fa outd=duplicate.fa uniqueonly=t e=10

            The run dedupe again on the duplicates:

            dedupe.sh in=duplicate.fa out=core.fa e=10

            This is not a perfect solution, but it will give you a file with exactly one copy each of all the contigs that appear at least twice in the input.

            -Brian

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM
            • seqadmin
              The Impact of AI in Genomic Medicine
              by seqadmin



              Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
              02-26-2024, 02:07 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-14-2024, 06:13 AM
            0 responses
            32 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-08-2024, 08:03 AM
            0 responses
            71 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-07-2024, 08:13 AM
            0 responses
            80 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-06-2024, 09:51 AM
            0 responses
            68 views
            0 likes
            Last Post seqadmin  
            Working...
            X